PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Pavir.7NG011500.1.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family C3H
Protein Properties Length: 560aa    MW: 61110.4 Da    PI: 7.204
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.7NG011500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH17.57.3e-061031151426
                          --TTTTT-SS-SS CS
              zf-CCCH  14 tCkyGdrCkFaHg 26 
                           CkyG +C+F+H+
  Pavir.7NG011500.1.p 103 SCKYGTSCRFSHD 115
                          7***********6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS501039.07591117IPR000571Zinc finger, CCCH-type
PROSITE profilePS501037.244130155IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:3.20.20.705.3E-68327556IPR013785Aldolase-type TIM barrel
SuperFamilySSF513955.23E-54331558No hitNo description
CDDcd028011.31E-89331556No hitNo description
PfamPF012071.7E-49334557IPR001269tRNA-dihydrouridine synthase
PROSITE patternPS011360415433IPR018517tRNA-dihydrouridine synthase, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008033Biological ProcesstRNA processing
GO:0055114Biological Processoxidation-reduction process
GO:0017150Molecular FunctiontRNA dihydrouridine synthase activity
GO:0046872Molecular Functionmetal ion binding
GO:0050660Molecular Functionflavin adenine dinucleotide binding
Sequence ? help Back to Top
Protein Sequence    Length: 560 aa     Download sequence    Send to blast
MAATAPATDP PDSSPAVTTD SPPPPRPSPE ELVARAVAPV KPAFLRPPPI REVPKEEGKA  60
AGGGAVVTGE KKSKRQLKRE RQQEQKSASH LCIEVGKSGN VDSCKYGTSC RFSHDINAYL  120
AQKPGDLEGT CPFTMLGQLC PYGLTCRFLG THKDNLAPQN HSEGNHERNP LSKDIQKLLW  180
KNKYKFPKAS AQIKLLGLKD GNKNKAKAAN DDNPDEACEL NDDDKTESLS CIPVNVEPDP  240
TLCKEINNSE GEPLVVSSVQ CVEPRPLKKS KVEVDETLND GTGIHDNGAE SEDLNLINGI  300
KVSSNNQSSC RVDLITTPHL REKKIIDFRE KLYLAPLTTV GNLPFRRLCK TLGADITCGE  360
MAMCTNLLQG QASEWALLRR HPSEDLFGVQ ICGPYPDTVA RTVELVDNEC SVDFIDINMG  420
CPIDIVVNKG AGSSLLTKPM RIKSIVQAAS TVTEKLLTVK VRTAFFEGRN RADSIVSDIY  480
DWGASAITIH GRSRQQRYSK LADWDYIYQC AQKAPDNLHV IGNGDVFSFT DWNKHISDCS  540
KISTCMIARG ALIKPAHPG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ei9_A1e-2232855527250tRNA-dihydrouridine synthase B
6ei9_B1e-2232855527250tRNA-dihydrouridine synthase B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.71460.0callus| leaf| root| stem
Functional Description ? help Back to Top
Source Description
UniProtCatalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.7NG011500.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0678840.0BT067884.1 Zea mays full-length cDNA clone ZM_BFc0185C01 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025824565.10.0tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like isoform X2
SwissprotQ7XT070.0DUS3L_ORYSJ; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
TrEMBLA0A3L6QB050.0A0A3L6QB05_PANMI; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
STRINGPavir.J29517.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP103222527
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]